scater_gui {scater} | R Documentation |
scater shiny app GUI for workflow for less programmatically inclined users or those who would like a quick and easy way to view multiple plots.
scater_gui(object)
object |
SinglCellExperiment object after running |
Opens a browser window with an interactive shiny app and visualize all possible plots included in the scater
Davis McCarthy and Vladimir Kiselev
data("sc_example_counts") data("sc_example_cell_info") example_sce <- SingleCellExperiment( assays = list(counts = sc_example_counts), colData = sc_example_cell_info) example_sce <- normalize(example_sce) drop_genes <- apply(exprs(example_sce), 1, function(x) {var(x) == 0}) example_sce <- example_sce[!drop_genes, ] example_sce <- calculateQCMetrics(example_sce, feature_controls = list(set1 = 1:40)) ## Not run: scater_gui(example_sce) ## End(Not run)